The relevant question as I see it is :
Can you reset the depth after locking on to the target? If so, then no problem...right?...just remember to do it.
For the life of me I can't recall the sim doing this when I used auto targeting.
Of Course, come to think of it...I doubt if I was in the torpedo setting mode when I was acquiring a target lock. Probably I always did the settings first. Then aquired the target. It is entirely possible that it was doing this and I simply did not notice it. I do remember though that I stated once in a thread, that I got a lot more hits, and sinkings, when I set all depths to 5 feet no matter the target keel depth. Historically many American torpedos ran deeper than their setting and my impression was that the sim was trying to model this. I was simply correcting for that by setting to 5 feet depth..but then if the L lock changed the setting???...who knows???